SMTL ID : 4nln.1

Structure of human DNA polymerase beta complexed with nicked DNA containing a template 8BrG and incoming CTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: 5'-D(P*GP*TP*CP*GP*G)-3'(Non-covalent)

DG-DT-DC-DG-DG.1: 19 residues within 4Å: Chain A: H.28, K.29, A.32, Y.33, L.56, P.57, G.58, V.59, G.60, T.61, K.62, I.63, K.66 Chain B: C.1, C.2, G.3, A.4, C.5 Ligands: NA.4 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.28

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: S.165 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.165, H2O.1 MG.6: 4 residues within 4Å: Chain A: D.184, D.186 Chain C: C.11 Ligands: PO4.5 No protein-ligand interaction detected (PLIP)

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain A: T.95, V.97, S.98, G.99, I.100 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.97, A:G.99, A:I.100 NA.4: 5 residues within 4Å: Chain A: K.54, K.55, L.56, V.59 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.59, A:V.59

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 6 residues within 4Å: Chain A: G.173, S.174, S.182, G.183, D.184 Ligands: MG.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.174, A:S.174, A:S.174, A:G.183, A:D.184, A:D.184, A:D.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koag, M.C. et al., Structural basis for promutagenicity of 8-halogenated Guanine. J.Biol.Chem. (2014)

Release Date

2014-01-22

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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